You can try and drag the grey triangle at the bottom left (next to the search field) to resize the window
or
close WeakAura's configuration window and enter the following script into Chat:
Code:
/run WeakAurasSaved.frame = {xOffset = -480, yOffset = -230, height = 500, width = 630,}
If this doesn't help because there is an error with one of your auras, activate the LUA error display under
Interface > Help > Display Lua Errors
or via
Code:
/run SetCVar("scriptErrors", 1) ReloadUI()
AddOn configurations are stored in the WTF/Account-Folder.